-
1
-
-
84903516439
-
Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing
-
Hovestadt, V. et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 510, 537-541 (2014).
-
(2014)
Nature
, vol.510
, pp. 537-541
-
-
Hovestadt, V.1
-
2
-
-
84864419974
-
Dissecting the genomic complexity underlying medulloblastoma
-
Jones, D. T. et al. Dissecting the genomic complexity underlying medulloblastoma. Nature 488, 100-105 (2012).
-
(2012)
Nature
, vol.488
, pp. 100-105
-
-
Jones, D.T.1
-
3
-
-
84896096387
-
Genome sequencing of SHH medulloblastoma predicts genotyperelated response to smoothened inhibition
-
Kool, M. et al. Genome sequencing of SHH medulloblastoma predicts genotyperelated response to smoothened inhibition. Cancer Cell 25, 393-405 (2014).
-
(2014)
Cancer Cell
, vol.25
, pp. 393-405
-
-
Kool, M.1
-
4
-
-
84904816744
-
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
-
Northcott, P. A. et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428-434 (2014).
-
(2014)
Nature
, vol.511
, pp. 428-434
-
-
Northcott, P.A.1
-
5
-
-
84864425646
-
Subgroup-specific structural variation across 1,000 medulloblastoma genomes
-
Northcott, P. A. et al. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature 488, 49-56 (2012).
-
(2012)
Nature
, vol.488
, pp. 49-56
-
-
Northcott, P.A.1
-
6
-
-
84864492215
-
Medulloblastoma exome sequencing uncovers subtypespecific somatic mutations
-
Pugh, T. J. et al. Medulloblastoma exome sequencing uncovers subtypespecific somatic mutations. Nature 488, 106-110 (2012).
-
(2012)
Nature
, vol.488
, pp. 106-110
-
-
Pugh, T.J.1
-
7
-
-
84862776537
-
Clonal selection drives genetic divergence of metastatic medulloblastoma
-
Wu, X. et al. Clonal selection drives genetic divergence of metastatic medulloblastoma. Nature 482, 529-533 (2012).
-
(2012)
Nature
, vol.482
, pp. 529-533
-
-
Wu, X.1
-
8
-
-
84904895951
-
Impact of craniospinal dose, boost volume, and neurologic complications on intellectual outcome in patients with medulloblastoma
-
Moxon-Emre, I. et al. Impact of craniospinal dose, boost volume, and neurologic complications on intellectual outcome in patients with medulloblastoma. J. Clin. Oncol. 32, 1760-1768 (2014).
-
(2014)
J. Clin. Oncol.
, vol.32
, pp. 1760-1768
-
-
Moxon-Emre, I.1
-
9
-
-
84862270168
-
The clinical implications of medulloblastoma subgroups
-
Northcott, P. A., Korshunov, A., Pfister, S. M. & Taylor, M. D. The clinical implications of medulloblastoma subgroups. Nature Rev. Neurol. 8, 340-351 (2012).
-
(2012)
Nature Rev. Neurol.
, vol.8
, pp. 340-351
-
-
Northcott, P.A.1
Korshunov, A.2
Pfister, S.M.3
Taylor, M.D.4
-
10
-
-
84870215426
-
Medulloblastomics: The end of the beginning
-
Northcott, P. A. et al. Medulloblastomics: the end of the beginning. Nature Rev. Cancer 12, 818-834 (2012).
-
(2012)
Nature Rev. Cancer
, vol.12
, pp. 818-834
-
-
Northcott, P.A.1
-
11
-
-
84886725191
-
Recurrence patterns across medulloblastoma subgroups: An integrated clinical and molecular analysis
-
Ramaswamy, V. et al. Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis. Lancet Oncol. 14, 1200-1207 (2013).
-
(2013)
Lancet Oncol.
, vol.14
, pp. 1200-1207
-
-
Ramaswamy, V.1
-
12
-
-
78751644099
-
Genetic variegation of clonal architecture and propagating cells in leukaemia
-
Anderson, K. et al. Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature 469, 356-361 (2011).
-
(2011)
Nature
, vol.469
, pp. 356-361
-
-
Anderson, K.1
-
13
-
-
84884365015
-
The causes and consequences of genetic heterogeneity in cancer evolution
-
Burrell, R. A., McGranahan, N., Bartek, J. & Swanton, C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature 501, 338-345 (2013).
-
(2013)
Nature
, vol.501
, pp. 338-345
-
-
Burrell, R.A.1
McGranahan, N.2
Bartek, J.3
Swanton, C.4
-
14
-
-
84862776906
-
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
-
Ding, L. et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481, 506-510 (2012).
-
(2012)
Nature
, vol.481
, pp. 506-510
-
-
Ding, L.1
-
15
-
-
84856013431
-
Clonal evolution in cancer
-
Greaves, M. & Maley, C. C. Clonal evolution in cancer. Nature 481, 306-313 (2012).
-
(2012)
Nature
, vol.481
, pp. 306-313
-
-
Greaves, M.1
Maley, C.C.2
-
16
-
-
84874102335
-
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia
-
Landau, D. A. et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152, 714-726 (2013).
-
(2013)
Cell
, vol.152
, pp. 714-726
-
-
Landau, D.A.1
-
17
-
-
57149118627
-
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia
-
Mullighan, C. G. et al. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science 322, 1377-1380 (2008).
-
(2008)
Science
, vol.322
, pp. 1377-1380
-
-
Mullighan, C.G.1
-
18
-
-
84892373020
-
Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma
-
Johnson, B. E. et al. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science 343, 189-193 (2014).
-
(2014)
Science
, vol.343
, pp. 189-193
-
-
Johnson, B.E.1
-
19
-
-
70349969478
-
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
-
Shah, S. P. et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809-813 (2009).
-
(2009)
Nature
, vol.461
, pp. 809-813
-
-
Shah, S.P.1
-
20
-
-
77958014613
-
How darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine
-
Gerlinger, M. & Swanton, C. How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine. Br. J. Cancer 103, 1139-1143 (2010).
-
(2010)
Br. J. Cancer
, vol.103
, pp. 1139-1143
-
-
Gerlinger, M.1
Swanton, C.2
-
21
-
-
84925229458
-
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
-
Eirew, P. et al. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature 518, 422-426 (2015).
-
(2015)
Nature
, vol.518
, pp. 422-426
-
-
Eirew, P.1
-
22
-
-
84873084388
-
Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer
-
Kreso, A. et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science 339, 543-548 (2013).
-
(2013)
Science
, vol.339
, pp. 543-548
-
-
Kreso, A.1
-
23
-
-
78751661556
-
Evolution of human BCR-ABL1 lymphoblastic leukaemiainitiating cells
-
Notta, F. et al. Evolution of human BCR-ABL1 lymphoblastic leukaemiainitiating cells. Nature 469, 362-367 (2011).
-
(2011)
Nature
, vol.469
, pp. 362-367
-
-
Notta, F.1
-
24
-
-
84867115500
-
Functional genomics identifies drivers of medulloblastoma dissemination
-
Mumert, M. et al. Functional genomics identifies drivers of medulloblastoma dissemination. Cancer Res. 72, 4944-4953 (2012).
-
(2012)
Cancer Res.
, vol.72
, pp. 4944-4953
-
-
Mumert, M.1
-
25
-
-
80052765869
-
Novel molecular and computational methods improve the accuracy of insertion site analysis in sleeping beauty-induced tumors
-
Brett, B. T. et al. Novel molecular and computational methods improve the accuracy of insertion site analysis in Sleeping Beauty-induced tumors. PLoS ONE 6, e24668 (2011).
-
(2011)
PLoS ONE
, vol.6
, pp. e24668
-
-
Brett, B.T.1
-
26
-
-
22444444402
-
Cancer gene discovery in solid tumours using transposon-based somatic mutagenesis in the mouse
-
Collier, L. S., Carlson, C. M., Ravimohan, S., Dupuy, A. J. & Largaespada, D. A. Cancer gene discovery in solid tumours using transposon-based somatic mutagenesis in the mouse. Nature 436, 272-276 (2005).
-
(2005)
Nature
, vol.436
, pp. 272-276
-
-
Collier, L.S.1
Carlson, C.M.2
Ravimohan, S.3
Dupuy, A.J.4
Largaespada, D.A.5
-
27
-
-
22444431606
-
Mammalian mutagenesis using a highly mobile somatic sleeping beauty transposon system
-
Dupuy, A. J., Akagi, K., Largaespada, D. A., Copeland, N. G. & Jenkins, N. A. Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system. Nature 436, 221-226 (2005).
-
(2005)
Nature
, vol.436
, pp. 221-226
-
-
Dupuy, A.J.1
Akagi, K.2
Largaespada, D.A.3
Copeland, N.G.4
Jenkins, N.A.5
-
28
-
-
84885423998
-
Subgroup-specific prognostic implications of TP53 mutation in medulloblastoma
-
Zhukova, N. et al. Subgroup-specific prognostic implications of TP53 mutation in medulloblastoma. J. Clin. Oncol. 31, 2927-2935 (2013).
-
(2013)
J. Clin. Oncol.
, vol.31
, pp. 2927-2935
-
-
Zhukova, N.1
-
29
-
-
84867301331
-
The bHLH repressor deadpan regulates the self-renewal and specification of drosophila larval neural stem cells independently of notch
-
Zhu, S. et al. The bHLH repressor Deadpan regulates the self-renewal and specification of Drosophila larval neural stem cells independently of Notch. PLoS ONE 7, e46724 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e46724
-
-
Zhu, S.1
-
30
-
-
20244385424
-
Drosophila p53 is a structural and functional homolog of the tumor suppressor p53
-
Ollmann, M. et al. Drosophila p53 is a structural and functional homolog of the tumor suppressor p53. Cell 101, 91-101 (2000).
-
(2000)
Cell
, vol.101
, pp. 91-101
-
-
Ollmann, M.1
-
31
-
-
84869235386
-
-
Technical Report No
-
Fraley, C., Raftery, E. A., Murphy, T. B. & Scrucca, L. mclust Version 4 for R: Normal Mixture Modeling for Model-Based Clustering, Classification, and Density Estimation. Technical Report No. 597 (2012).
-
(2012)
Mclust Version 4 for R: Normal Mixture Modeling for Model-Based Clustering, Classification, and Density Estimation
-
-
Fraley, C.1
Raftery, E.A.2
Murphy, T.B.3
Scrucca, L.4
-
32
-
-
84892621211
-
TERT promoter mutations are highly recurrent in SHH subgroup medulloblastoma
-
Remke, M. et al. TERT promoter mutations are highly recurrent in SHH subgroup medulloblastoma. Acta Neuropathol. 126, 917-929 (2013).
-
(2013)
Acta Neuropathol
, vol.126
, pp. 917-929
-
-
Remke, M.1
-
33
-
-
84899054169
-
Shatter proof: Operational detection and quantification of chromothripsis
-
Govind, S. K. et al. Shatter Proof: operational detection and quantification of chromothripsis. BMC Bioinformatics 15, 78 (2014).
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 78
-
-
Govind, S.K.1
-
34
-
-
84888862866
-
DGIdb: Mining the druggable genome
-
Griffith, M. et al. DGIdb: mining the druggable genome. Nature Methods 10, 1209-1210 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 1209-1210
-
-
Griffith, M.1
-
35
-
-
84964240053
-
Perspective biological and therapeutic impact of intratumor heterogeneity in cancer evolution
-
McGranahan, N. & Swanton, C. Perspective biological and therapeutic impact of intratumor heterogeneity in cancer evolution. Cancer Cell 27, 15-26 (2015).
-
(2015)
Cancer Cell
, vol.27
, pp. 15-26
-
-
McGranahan, N.1
Swanton, C.2
-
36
-
-
84891370404
-
EXPANDS: Expanding ploidy and allele frequency on nested subpopulations
-
Andor, N., Harness, J. V., Müller, S., Mewes, H. W. & Petritsch, C. EXPANDS: expanding ploidy and allele frequency on nested subpopulations. Bioinformatics 30, 50-60 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 50-60
-
-
Andor, N.1
Harness, J.V.2
Müller, S.3
Mewes, H.W.4
Petritsch, C.5
-
37
-
-
33645396945
-
Genetic clonal diversity predicts progression to esophageal adenocarcinoma
-
Maley, C. C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nature Genet. 38, 468-473 (2006).
-
(2006)
Nature Genet.
, vol.38
, pp. 468-473
-
-
Maley, C.C.1
-
38
-
-
84897954204
-
PyClone: Statistical inference of clonal population structure in cancer
-
Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nature Methods 11, 396-398 (2014).
-
(2014)
Nature Methods
, vol.11
, pp. 396-398
-
-
Roth, A.1
-
39
-
-
84922235074
-
Combined myc and p53 defects emerge at medulloblastoma relapse and define rapidly progressive, therapeutically targetable disease
-
Hill, R. M. et al. Combined Myc and p53 defects emerge at medulloblastoma relapse and define rapidly progressive, therapeutically targetable disease. Cancer Cell 27, 72-84 (2015).
-
(2015)
Cancer Cell
, vol.27
, pp. 72-84
-
-
Hill, R.M.1
-
40
-
-
84925483142
-
Medulloblastoma subgroups remain stable across primary and metastatic compartments
-
Wang, X. et al. Medulloblastoma subgroups remain stable across primary and metastatic compartments. Acta Neuropathol. 129, 449-457 (2015).
-
(2015)
Acta Neuropathol
, vol.129
, pp. 449-457
-
-
Wang, X.1
-
41
-
-
84874354257
-
The implications of clonal genome evolution for cancer medicine
-
Aparicio, S. & Caldas, C. The implications of clonal genome evolution for cancer medicine. N. Engl. J. Med. 368, 842-851 (2013).
-
(2013)
N. Engl. J. Med.
, vol.368
, pp. 842-851
-
-
Aparicio, S.1
Caldas, C.2
-
42
-
-
4043075127
-
Cancer prevention strategies that address the evolutionary dynamics of neoplastic cells: Simulating benign cell boosters and selection for chemosensitivity
-
Maley, C. C., Reid, B. J. & Forrest, S. Cancer prevention strategies that address the evolutionary dynamics of neoplastic cells: simulating benign cell boosters and selection for chemosensitivity. Cancer Epidemiol. Biomarkers Prev. 13, 1375-1384 (2004).
-
(2004)
Cancer Epidemiol. Biomarkers Prev.
, vol.13
, pp. 1375-1384
-
-
Maley, C.C.1
Reid, B.J.2
Forrest, S.3
-
43
-
-
79551673399
-
Characterization of image quality and image-guidance performance of a preclinical microirradiator
-
Clarkson, R. et al. Characterization of image quality and image-guidance performance of a preclinical microirradiator. Med. Phys. 38, 845-856 (2011).
-
(2011)
Med. Phys.
, vol.38
, pp. 845-856
-
-
Clarkson, R.1
-
44
-
-
0034973266
-
AAPM protocol for 40-300 kV X-ray beam dosimetry in radiotherapy and radiobiology
-
Ma, C. M. et al. AAPM protocol for 40-300 kV X-ray beam dosimetry in radiotherapy and radiobiology. Med. Phys. 28, 868-893 (2001).
-
(2001)
Med. Phys.
, vol.28
, pp. 868-893
-
-
Ma, C.M.1
-
45
-
-
67649884743
-
Fast and accurate short read alignment with burrows-wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
46
-
-
77956295988
-
The genome analysis toolkit: A map reduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A. et al. The genome analysis toolkit: a Map Reduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
47
-
-
84876030710
-
Using drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, snp sift
-
Cingolani, P. et al. Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, Snp Sift. Front. Genet. 3, http://dx.doi.org/10.3389/fgene.2012.00035 (2012).
-
(2012)
Front. Genet.
, vol.3
-
-
Cingolani, P.1
-
48
-
-
84864153492
-
Strelka: Accurate somatic small-variant calling from sequenced tumour-normal sample pairs
-
Saunders, C. T. et al. Strelka: Accurate somatic small-variant calling from sequenced tumour-normal sample pairs. Bioinformatics 28, 1811-1817 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1811-1817
-
-
Saunders, C.T.1
-
49
-
-
68549104404
-
The sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
50
-
-
84876786068
-
EMu: Probabilistic inference of mutational processes and their localization in the cancer genome
-
Fischer, A., Illingworth, C. J., Campbell, P. J. & Mustonen, V. EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biol. 14, R39 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R39
-
-
Fischer, A.1
Illingworth, C.J.2
Campbell, P.J.3
Mustonen, V.4
-
51
-
-
77955293476
-
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
-
Jones, S. J. et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 11, R82 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R82
-
-
Jones, S.J.1
-
52
-
-
33747890138
-
Integrating copy number polymorphisms into array CGH analysis using a robust HMM
-
Shah, S. P. et al. Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics 22, 431-439 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 431-439
-
-
Shah, S.P.1
-
53
-
-
84856561659
-
Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data
-
Boeva, V. et al. Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28, 423-425 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 423-425
-
-
Boeva, V.1
-
54
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
Rozen, S. & Skaletsky, H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132, 365-386 (2000).
-
(2000)
Methods Mol. Biol.
, vol.132
, pp. 365-386
-
-
Rozen, S.1
Skaletsky, H.2
-
55
-
-
84874025843
-
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
-
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnol. 31, 213-219 (2013).
-
(2013)
Nature Biotechnol
, vol.31
, pp. 213-219
-
-
Cibulskis, K.1
-
56
-
-
84904264545
-
+ cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma
-
+cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma. Cancer Cell 26, 33-47 (2014).
-
(2014)
Cancer Cell
, vol.26
, pp. 33-47
-
-
Vanner, R.J.1
-
57
-
-
84899684426
-
Cytogenetic prognostication within medulloblastoma subgroups
-
Shih, D. J. H. et al. Cytogenetic prognostication within medulloblastoma subgroups. J. Clin. Oncol. 32, 886-896 (2014).
-
(2014)
J. Clin. Oncol.
, vol.32
, pp. 886-896
-
-
Shih, D.J.H.1
-
58
-
-
79954991010
-
Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome
-
Cho, Y.-J. et al. Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome. J. Clin. Oncol. 29, 1424-1430 (2011).
-
(2011)
J. Clin. Oncol.
, vol.29
, pp. 1424-1430
-
-
Cho, Y.-J.1
-
59
-
-
84904917064
-
JAGuaR: Junction alignments to genome for RNA-seq reads
-
Butterfield, Y. S. et al. JAGuaR: junction alignments to genome for RNA-seq reads. PLoS ONE 9, e102398 (2014).
-
(2014)
PLoS ONE
, vol.9
, pp. e102398
-
-
Butterfield, Y.S.1
-
60
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
|